RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1122
(150 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 84.7 bits (210), Expect = 4e-22
Identities = 36/117 (30%), Positives = 60/117 (51%), Gaps = 7/117 (5%)
Query: 11 IFQECQPEFLHDLVLKMKAYIFTPGDLICRKGEVAREMFIIADGILEVI--SESGR--VL 66
+F E L +L ++ F G++I R+G+ A ++I+ G +EV E GR ++
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 67 TTMKAGDFFGEIGILNLDGLNKRTADVRSVGYAELFSLSREDVLSAMKDYPEAQEIL 123
+ GD FGE+ +L R+A VR++ +EL L R D +++YPE L
Sbjct: 61 GFLGPGDLFGELALLGNG---PRSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 80.9 bits (200), Expect = 1e-20
Identities = 29/117 (24%), Positives = 54/117 (46%), Gaps = 5/117 (4%)
Query: 11 IFQECQPEFLHDLVLKMKAYIFTPGDLICRKGEVAREMFIIADGILEVISES----GRVL 66
+F+ E L +L ++ + G++I R+G+V +II G +EV +++
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIV 60
Query: 67 TTMKAGDFFGEIGILNLDGLNKRTADVRSVGYAELFSLSREDVLSAMKDYPEAQEIL 123
T+ GDFFGE+ +L +A ++ A L + D L + + P+ L
Sbjct: 61 GTLGPGDFFGELALLTNSRRA-ASAAAVALELATLLRIDFRDFLQLLPELPQLLLEL 116
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 68.5 bits (168), Expect = 4e-16
Identities = 32/91 (35%), Positives = 53/91 (58%), Gaps = 7/91 (7%)
Query: 32 FTPGDLICRKGEVAREMFIIADGILEV--ISESGR--VLTTMKAGDFFGEIGILNLDGLN 87
F G++I R+G+ A ++I+ G ++V + E GR +L + GDFFGE+ +L G
Sbjct: 4 FKKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALL---GGE 60
Query: 88 KRTADVRSVGYAELFSLSREDVLSAMKDYPE 118
R+A V ++ +EL + RED L ++ PE
Sbjct: 61 PRSATVVALTDSELLVIPREDFLELLEQDPE 91
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 58.7 bits (142), Expect = 3e-11
Identities = 37/130 (28%), Positives = 66/130 (50%), Gaps = 7/130 (5%)
Query: 9 VTIFQECQPEFLHDLVLKMKAYIFTPGDLICRKGEVAREMFIIADGILEV--ISESGR-- 64
+ E L L LK++ G+++ +GE A ++II GI+++ +E GR
Sbjct: 5 NPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGREI 64
Query: 65 VLTTMKAGDFFGEIGILNLDGLNKRTADVRSVGYAELFSLSREDVLSAMKDYPEAQEILQ 124
+L + GDFFGE+ +L G + R+A ++ E+ + R+D L + + P+ L
Sbjct: 65 ILGFLGPGDFFGELALL---GGDPRSASAVALTDVEVLEIPRKDFLELLAESPKLALALL 121
Query: 125 NLGRKRLMEA 134
L +RL +A
Sbjct: 122 RLLARRLRQA 131
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 46.8 bits (111), Expect = 1e-06
Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 6/113 (5%)
Query: 9 VTIFQECQPEFLHDLVLKMKAYIFTPGDLICRKGEVAREMFIIADGILEVISESG---RV 65
V +F+ E L LV KMKA P + + + E +++I+ G +E+I G RV
Sbjct: 379 VYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERV 438
Query: 66 LTTMKAGDFFGEIGILNLDGLNKRTADVRSVGYAELFSLSREDVLSAMKDYPE 118
+ T+ GD FGE+G L ++ R+ ++L L ++ AM+ E
Sbjct: 439 VGTLGCGDIFGEVGALC---CRPQSFTFRTKTLSQLLRLKTSTLIEAMQTRQE 488
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 42.7 bits (101), Expect = 2e-05
Identities = 33/123 (26%), Positives = 56/123 (45%), Gaps = 9/123 (7%)
Query: 12 FQECQPEFLHDLVLKMKAYIFTPGDLICRKGEVAREMFIIADGILEVISESGRVLTTMKA 71
F + E L L+ ++ + G++I G +++I G++EV S+ G VL + A
Sbjct: 15 FSQLPAEELEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGGEVLDRLAA 74
Query: 72 GDFFGEIGILNLDGLNKR---TADVRSVGYAELFSLSREDVLSAMKDYPEAQEILQNLGR 128
GD FG + LNK+ A+ S+ Y L + + M++ PE +
Sbjct: 75 GDLFGFSSL--FTELNKQRYMAAEEDSLCYL----LPKSVFMQLMEENPEFADFFLRSLA 128
Query: 129 KRL 131
KRL
Sbjct: 129 KRL 131
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 39.6 bits (93), Expect = 2e-04
Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 12/101 (11%)
Query: 38 ICRKGEVAREMFIIADGILEVISE--SGR--VLTTMKAGDFFGEIGILNLDGLNKRTADV 93
+ GE A ++ I G + V+ + G+ +L+ + GDF GE+G+ + +R+A V
Sbjct: 31 LIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGL--FEEGQERSAWV 88
Query: 94 RSVGYAELFSLSREDVLSAMKDYPEAQEILQNLGR---KRL 131
R+ E+ +S + ++ P +IL L +RL
Sbjct: 89 RAKTACEVAEISYKKFRQLIQVNP---DILMALSAQMARRL 126
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 34.7 bits (80), Expect = 0.010
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 32 FTPGDLICRKGEVAREMFIIADGILEVI---SESGRVLTTMKAGDFFG 76
+ G+ + R+GE ++ I G EV E R +K D+FG
Sbjct: 36 YGKGEYVVREGEPGDGLYFIWKGEAEVSGPAEEESRPEFLLKRYDYFG 83
>gnl|CDD|236322 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 368
Score = 30.2 bits (69), Expect = 0.42
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 75 FGEIGILNLDGLNKRTADVRSVGYAELFSLSREDVLSAMKD-YPEAQEILQNLGRKRLME 133
G +G+LNL+GL R D + E+ SL +++ M++ Y A+ I L +R+ E
Sbjct: 70 LGGLGVLNLEGLWTRYEDPEPI-LDEIASLGKDEATRLMQELY--AEPIKPELITERIAE 126
Query: 134 AK 135
+
Sbjct: 127 IR 128
>gnl|CDD|236871 PRK11175, PRK11175, universal stress protein UspE; Provisional.
Length = 305
Score = 28.7 bits (65), Expect = 1.1
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 7/23 (30%)
Query: 21 HDLVLKM-------KAYIFTPGD 36
HDLV+KM ++ IFTP D
Sbjct: 108 HDLVVKMTHQHDKLESVIFTPTD 130
>gnl|CDD|234862 PRK00912, PRK00912, ribonuclease P protein component 3;
Provisional.
Length = 237
Score = 27.3 bits (61), Expect = 2.9
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 92 DVRS----VGYAELFSLSREDVLSAMKDYPEAQEILQNLGRKRLM 132
D+RS + AELF + ++ L A+ YPE I++ ++
Sbjct: 181 DLRSPREMIALAELFGMEEDEALKALSYYPE--SIIKKNRNRKNY 223
>gnl|CDD|168961 PRK07473, PRK07473, carboxypeptidase; Provisional.
Length = 376
Score = 26.3 bits (58), Expect = 7.2
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 72 GDFFGEIGILNLDGLNKRTADVRSVG-YAELFSLSREDVLSA 112
G+F G +GI LDGL R AD ++ + E+ SL+ L A
Sbjct: 328 GNFTGAMGIPTLDGLGVRGADYHTLNEHIEVDSLAERGRLMA 369
>gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta
subunit. Dissimilatory sulfite reductase catalyzes the
six-electron reduction of sulfite to sulfide, as the
terminal reaction in dissimilatory sulfate reduction.
It remains unclear however, whether trithionate and
thiosulfate serve as intermediate compounds to sulfide,
or as end products of sulfite reduction. Sulfite
reductase is a multisubunit enzyme composed of dimers
of either alpha/beta or alpha/beta/gamma subunits, each
containing a siroheme and iron sulfur cluster
prosthetic center. Found in sulfate-reducing bacteria,
these genes are commonly located in an unidirectional
gene cluster. This model describes the beta subunit of
sulfite reductase [Central intermediary metabolism,
Sulfur metabolism].
Length = 341
Score = 26.0 bits (57), Expect = 8.3
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 50 IIADGILEVISESGRVLTTMKAGDFFGEIGILNLDGLNK--RTADVRSVGY 98
++ G+++ ++ESG V+ T+KA G +L++D L K AD S GY
Sbjct: 14 VVKPGVIKHVAESGDVIYTVKA----GTPRLLSVDTLRKLCDIADKYSDGY 60
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 24.5 bits (54), Expect = 9.1
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 94 RSVGYAELFSLSREDVLSAMKDY 116
RS+G A++ R D L AMK Y
Sbjct: 39 RSLGTADVVFERRADALKAMKQY 61
>gnl|CDD|233105 TIGR00728, OPT_sfam, oligopeptide transporter, OPT superfamily.
This superfamily has two main branches. One branch
contains a tetrapeptide transporter demonstrated
experimentally in three different species of yeast. The
other family contains EspB of Myxococcus xanthus, a
protein required for normal rather than delayed
sporulation after cellular aggregation; its role is
unknown but is compatible with transport of a signalling
molecule. Homology between the two branches of the
superfamily is seen most easily at the ends of the
protein. The central regions are poorly conserved within
each branch and may not be homologous between branches.
Length = 606
Score = 26.2 bits (58), Expect = 9.5
Identities = 8/54 (14%), Positives = 15/54 (27%), Gaps = 3/54 (5%)
Query: 27 MKAYIFTPGDLICRKGEVAREMFIIADGILEVISESGRVLTTMKAGDFFGEIGI 80
A + C V +I I I + + +F +G+
Sbjct: 465 YHAIGNQNNNFTCPNALVFFNASLIWGVIGPKIFSGKGLYCGLM---WFFLVGV 515
>gnl|CDD|239648 cd03676, Nudix_hydrolase_3, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes belong
to this superfamily requires a divalent cation, such as
Mg2+ or Mn2+, for their activity and contain a highly
conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where
U = I, L or V), which functions as a metal binding and
catalytic site. Substrates of nudix hydrolases include
intact and oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
& "house-cleaning" enzymes. Substrate specificity is
used to define families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 180
Score = 25.7 bits (57), Expect = 9.9
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 19/74 (25%)
Query: 6 VGVVTIFQECQPEFLHDLVLKMKAYIFT---PGDLI--CRKGEVAREMFIIADGILEVIS 60
VGVV+ +E + L V Y++ P D I + GEV E F + I
Sbjct: 105 VGVVSYLREGEAGGLQPEVE----YVYDLELPPDFIPAPQDGEV--ESFRLLT-----ID 153
Query: 61 ESGRVLTTMKAGDF 74
E VL +K G+F
Sbjct: 154 E---VLRALKEGEF 164
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.140 0.391
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,705,689
Number of extensions: 727475
Number of successful extensions: 715
Number of sequences better than 10.0: 1
Number of HSP's gapped: 705
Number of HSP's successfully gapped: 43
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)